MWNautilus comments

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                                            MWNautilus

ValueError: Minimization failed after 100 attempts.

Something similar here: issue with AMBER relaxation step: ``` AMBER relaxation: 83% 5/6 [elapsed: 1:00:42 remaining: 11:07] --------------------------------------------------------------------------- ValueError Traceback (most recent call last) [](https://localhost:8080/#) in () 88 max_outer_iterations=3, 89...

ValueError: Minimization failed after 100 attempts.

...the same task can be executed without any issues in ColabFold, incl. the AMBER relaxation steps: https://github.com/sokrypton/ColabFold So, there is something selectively broken in the DeepMind Alphafold2 notebook, only. -Michael.

jax.tree_util.tree_multimap() is deprecated

Are you guys sure all these AMBER-related postings you have added still belong to the initial issue I had posted here in my first note? If not, please delete these...

Installation procedure not working for Ubuntu 20.04 LTS

I tried it and the ninja paket gets installed, but the bookworm installation still fails afterwards with the same error message saying that ninja is missing.

Request: pLDDT & pTMscore to be stored in downloaded results archive

Thanks Sergey for the quick reply. Regarding the AMBER relaxation runtimes: When using Google Colab, even with the more costly Google payment models there is a total runtime limit. For...

Question: Issue with automated model ranking in mmseqs notebook?

No comment?

Question: Issue with automated model ranking in mmseqs notebook?

Thanks for the feedback, Sergey.

adding rosettafold2na to colabfold

If possible that would be fantastic. Michael.